4RYX

Crystal structure of RPE65 in complex with emixustat and palmitate, P6522 crystal form

X-RAY DIFFRACTION

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Starting Model(s)

Initial Refinement Model(s)
Type	Source	Accession Code	Details
experimental model	PDB	4F3A

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, HANGING DROP	8.5	281	35% MPD, 200 mM (NH4)2SO4 and 100 mM Tris, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 281K

Crystal Properties
Matthews coefficient	Solvent content
3.23	61.98

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 177.766	α = 90
b = 177.766	β = 90
c = 86.58	γ = 120

Symmetry
Space Group	P 65 2 2

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS PILATUS 6M-F		2014-03-24	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	APS BEAMLINE 24-ID-C	0.97920	APS	24-ID-C

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2	50	97.7	0.08	10.3	3.3	53112	53110		-3

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2	2.13	98		0.1231	0.97	3.3

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Starting model	Resolution (High)	Resolution (Low)	Number Reflections (All)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (Observed)	R-Work	R-Free	R-Free Selection Details	Mean Isotropic B
X-RAY DIFFRACTION	rigid body refinement	THROUGHOUT	4F3A	2	44.15	53109	53109	2642	97.69	0.16672	0.16448	0.2099	RANDOM	41.771

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.01			-0.01		0.03

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_2_deg	31.115
r_dihedral_angle_3_deg	12.675
r_dihedral_angle_4_deg	12.134
r_long_range_B_refined	7.68
r_long_range_B_other	7.54
r_dihedral_angle_1_deg	6.693
r_scangle_other	5.281
r_mcangle_it	4.242
r_mcangle_other	4.242
r_scbond_it	3.415
r_scbond_other	3.415
r_mcbond_it	2.763
r_mcbond_other	2.761
r_angle_refined_deg	1.515
r_angle_other_deg	0.774
r_chiral_restr	0.092
r_bond_refined_d	0.012
r_gen_planes_refined	0.007
r_bond_other_d	0.001
r_gen_planes_other	0.001
r_nbd_refined
r_nbd_other
r_nbtor_refined
r_nbtor_other
r_xyhbond_nbd_refined
r_xyhbond_nbd_other
r_metal_ion_refined
r_metal_ion_other
r_symmetry_vdw_refined
r_symmetry_vdw_other
r_symmetry_hbond_refined
r_symmetry_hbond_other
r_symmetry_metal_ion_refined
r_symmetry_metal_ion_other
r_scangle_it
r_rigid_bond_restr
r_sphericity_free
r_sphericity_bonded

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	4113
Nucleic Acid Atoms
Solvent Atoms	391
Heterogen Atoms	67

Software

Software
Software Name	Purpose
XDS	data scaling
REFMAC	refinement
XDS	data reduction
REFMAC	phasing